From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects

Patricia Buendia, Shu Ning Hsu, Akira Chiba, John Tyree, Robert Loredo

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Recent findings of extensive alternative splicing events occurring in eukaryotic organisms have provided a possible explanation for the puzzling discrepancy between the number of genes and high genome complexity. Most alternative splicing events in eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as expressed sequence tags (EST) sequencing and microarrays. Exonic splicing regulatory sequences (ESRs) are cis-acting factor binding sites that regulate constitutive and alternative splicing. In this paper, we describe an in silico analysis pipeline to extract putative ESRs from EST splicing graphs and from a multiple alignment of 15 species of insects. Our method, E2E, combines graph analysis, phylogenetic measures and a sliding window approach that extracts conserved motifs using comparative analysis and the Welch's t statistic. We studied 100% conserved motifs as well as those obtained from our E2E method. We compared our results with a recent study on the alternatively spliced N-Cadherin gene in the Drosophila melanogaster. We also looked for homologous ESTs in mouse and human genome and found that about half of the putative ESRs in common between insects and mammals have a high statistical support (p<0.01).

Original languageEnglish (US)
Title of host publication2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
Pages46-51
Number of pages6
DOIs
StatePublished - Apr 14 2011
Event1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 - Orlando, FL, United States
Duration: Feb 3 2011Feb 5 2011

Publication series

Name2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011

Other

Other1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
CountryUnited States
CityOrlando, FL
Period2/3/112/5/11

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Keywords

  • Alternative splicing
  • Cis-acting
  • Comparative Analysis
  • ESRs
  • Motifs
  • Mutually exclusive exons
  • Regulatory elements
  • Sequence analysis
  • Splicing graphs

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Buendia, P., Hsu, S. N., Chiba, A., Tyree, J., & Loredo, R. (2011). From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects. In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 (pp. 46-51). [5729938] (2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011). https://doi.org/10.1109/ICCABS.2011.5729938